Officials at the Food and Drug Administration advised physicians Monday to temporarily stop using Rotarix, a vaccine commonly given to children to protect them against the stomach bug rotavirus, because it is contaminated with traces of a second virus.

The contaminant, called PCV-1, is a DNA virus that infects pigs and other species but is not known to cause illness in humans or any other animals. The virus appears to have come from the cell cultures used to make Rotarix.

“There is no evidence this poses a safety risk,” Margaret A. Hamburg, FDA commissioner, told reporters in a telephone briefing.

The contaminant was found by a team of independent researchers testing a new way to screen vaccines for impurities. Rotarix’s maker, the pharmaceutical company GlaxoSmithKline, was told of the finding in early February. Both it and the FDA have since confirmed the presence of PCV-1 in the vaccine, which is given in two oral doses to infants between 6 and 24 weeks old.

Hamburg said the FDA is not pulling Rotarix off the market, and that even asking doctors to suspend its use for the moment “was not an easy call.” After consulting with scientists at the National Institutes of Health, the Centers for Disease Control and Prevention, as well as officials at the Department of Health and Human Services, “We felt that the judicious thing to do was to make a pause and try to determine what this virus was doing in the vaccine and how it got there.”

Rotavirus can cause vomiting and watery diarrhea in infants and children. Globally, it is one of the more serious infections of infancy, causing about 500,000 deaths a year. While deaths number fewer than 100 in the United States, the virus was responsible for about 50,000 pediatric hospitalizations annually before the vaccine came into common use.

Rotarix was licensed in 2008. Another rotavirus vaccine, RotaTeq, made by Merck, came on the market in 2006. FDA officials suggested that pediatricians use it rather than Rotarix for the time being.

While the FDA is recommending that doctors avoid Rotarix, Hamburg said she realizes health agencies in other countries may not agree with that advice, especially if an alternative vaccine isn’t available.

Thomas Breuer, the chief medical officer of GSK Biologicals, said the pharmaceutical house “is committed to patient safety and to the highest manufacturing standards for all our vaccines and medicines,” according to a company statement.

A GSK spokeswoman, Sarah Alspach, said the company “has elected to stop distribution and shipment of Rotarix and will not accept customer orders . . . until further notice.” The vaccine is made at a plant in Belgium. Worldwide sales in 2009 were $440 million, with $118 million — or about 30 percent of the total — in the United States.

Alspach said the company “is now reviewing how best to replace, in a timely way, the cell bank and virus seeds used as base production material.” Preliminary tests of GSK’s inactivated polio vaccine, which is also made in cell culture, has not found the contaminating virus.

FDA officials said they were uncertain whether whole PCV-1 viruses were present in the vaccine or just pieces of DNA left over from the manufacturing process. The agency will convene a meeting of experts in about six weeks to review the results of its and GSK’s investigation.

Neither government nor company officials would identify the “academic researchers” who found the contaminants. Those scientists are reportedly preparing a scientific article on their new method of screening vaccines.

Rotarix is a “live” but weakened strain of rotavirus. Such vaccines are often harder to purify than ones containing only fragments of a virus. In a guide for manufacturers released last month, FDA regulators noted that “comprehensive testing and qualification of the biological starting materials and lot-by-lot testing for adventitious [unwanted] agents are particularly important” for such vaccines.

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